With the finishing of the human genome sequence, there are fundamental reasons to sequence the chimpanzee genome. First, the chimpanzee provides an excellent animal model for biomedical research of human diseases. Identifying fixed sequence variants responsible for differential gene expression may explain the different physiological responses to shared diseases such as HIV, cancer and Alzheimer's disease. The 98-99% DNA sequence similarity and the near identity of proteins between human and chimpanzee suggest species-specific gene regulations likely account for their biological distinctiveness such as cranial morphology and cognition. Additionally, comparison of human and chimpanzee polymorphism rates and fixed differences across the genome will indicate regions in which selective pressure may play a role in maintaining genomic integrity. Such regions are candidates for further investigation of their biological roles. Finally, comparisons to other non-human primates would indicate the lineage of origin in fixed differences, pinpointing regions involved in distinguishing humans from chimpanzees. For these comparative sequence studies, an understanding of the intraspecific genetic variation found within chimpanzee populations is required. Perlegen's microarray technology allows rapid, economical, and accurate determination of where and what sequence differences exist in highly conserved regions between human and chimpanzee genomes. [unreadable] [unreadable]